Channel-stacked 3D NAND flash memory is very promising candidate for the next-generation NAND flash memory. However, there is an inherent issue on cell size variation between stacked channels due to the declined etch slope. In this paper, the effect of the cell variation on the incremental step pulse programming (ISPP) characteristics is studied with 3D TCAD simulation. The ISPP slope degradation of elliptical channel is investigated. To solve that problem, a new programming method is proposed, and we can alleviate the $V_T$ variation among cells and reduce the total programming time.